Requirement Analysis (Backend)

SCAI-BIO / PDataViewer

Parkinsons Disease cohort landscape visualization

https://pdata.k8s.bio.scai.fraunhofer.de

Apache License 2.0

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Requirement Analysis (Backend) #4

Closed tiadams closed 3 months ago

tiadams commented 5 months ago

How many (and which) datasets will be included?
What needs to be computed based on these datasets (e.g. summary statistics, models, plots)?

tiadams commented 4 months ago

Datasets to be used:

pls add @Yasaminsali @mehmetcanay ?

LLM models to be implemented:

BioLORD
PubMedBERT

any more @mehmetcanay ?

Vector database for mapping:

Vectordatabase (Neo4J) @SCAI-BIO/biodev (together with Alphas Team?)
Harmonization Endpoint

Endpoints to access CDM:

summary statistics
List all cohorts
List all (reference) features
Rank cohorts based on the existence of certain features

Concept for a data model:

How do we store?
How do we query?

mehmetcanay commented 4 months ago

Datasets to be used:

Parkinson's Progression Markers Initiative (PPMI)¹
The Fox Investigation for New Discovery of Biomarkers (BioFIND)¹
LRRK2 Cohort Consortium (LCC)¹
The Luxembourg Parkinson's Study (LuxPARK)²
The Oxford Parkinson's Disease Center (OPDC)²
Tracking Parkinson's Study (PRoBaND)²
Fox Insight³
Deprenyl and tocopherol antioxidative therapy of parkinsonism (DATATOP)³

¹ Patient-level data is preprocessed, dictionary is mapped. ² We do not have access to the patient-level data, but the dictionary is mapped. ³ We have data access but have not been preprocessed, dictionary is mapped.